Journal of Computer-Aided Molecular Design

, Volume 29, Issue 4, pp 305–314 | Cite as

Introducing the ‘active search’ method for iterative virtual screening

  • Roman Garnett
  • Thomas Gärtner
  • Martin Vogt
  • Jürgen Bajorath


A method is introduced for sequential similarity searching for active compounds. Given a set of known actives and a screening database, a strategy is devised to optimally rank test compounds by observing the outcome of each iteration before selecting the next compound. This ‘active search’ approach is based upon Bayesian decision theory. A typical ranking procedure used in virtual compound screening corresponds to a myopic approximation to the optimal strategy. Exploratory active search represents a less-myopic approach and is shown to accurately identify a variety of active compounds in iterative virtual screening trials on 120 compound classes. Source code and data for the active search approach presented herein is made freely available.


Active search Iterative virtual screening Bayesian decision theory 



Part of this work was supported by the German Science Foundation (DFG) under the reference number GA 1615/1-1.


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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Roman Garnett
    • 1
  • Thomas Gärtner
    • 1
    • 2
  • Martin Vogt
    • 3
  • Jürgen Bajorath
    • 3
  1. 1.Institute of Computer Science IIIRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
  2. 2.Fraunhofer Institute for Intelligent Analysis and Information Systems IAISSankt AugustinGermany
  3. 3.Program Unit Chemical Biology and Medicinal Chemistry, Department of Life Science Informatics, B-IT, LIMESRheinische Friedrich-Wilhelms-Universität BonnBonnGermany

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